The American Cancer Society estimates the lifetime risk that an individual will develop cancer is 1 in 2 for men and 1 in 3 for women. The development of cancer, while still not completely understood, can be enhanced as a result of a variety of risk factors. For example, exposure to environmental factors (e.g., tobacco smoke) might trigger modifications in certain genes, thereby initiating cancer development. Alternatively, these genetic modifications may not require an exposure to environmental factors to become abnormal. Indeed, certain mutations (e.g., insertions, deletions, substitutions; etc.) or abnormally imprinted genes can be inherited from generation to generation, thereby imparting an individual with a genetic predisposition to develop cancer.
Currently, the survival rates for many cancers are on the rise. One reason for this success is improvement in the detection of cancer at a stage at which treatment can be effective. Indeed, it has been noted that one of the most effective means to survive cancer is to detect its presence as early as possible. According to the American Cancer Society, the relative survival rate for many cancers would increase by about 15% if individuals participated in regular cancer screenings. Therefore, it is becoming increasingly useful to develop novel diagnostic tools to detect the cancer either before it develops or at an as early stage of development as possible.
One popular way of detecting cancer early is to analyze the genetic makeup of an individual to detect the presence of or to measure expression levels of a marker gene(s) related to the cancer. For example, there are various diagnostic methods that analyze a certain gene or a pattern of genes to detect cancers of the breast, tongue, mouth, colon, rectum, cervix, prostate, testis, and skin. Recently, analyzing the activity of certain DNA-binding proteins, such as the CCCTC-binding factor (CTCF), has been found to be useful in diagnosing a cancer or a predisposition to a cancer (see, e.g., U.S. Pat. No. 5,972,643). CTCF and similar DNA-binding proteins can act as transcription factors which regulate gene expression, including genes involved in cell proliferation. Normally, CTCF inhibits cell proliferation; however, a partial loss of CTCF functions caused by abnormal methylation of certain CTCF target sites, or by zinc finger mutations, has been shown to be associated with cancer.
Recent efforts have brought together the fields of genomic imprinting, DNA methylation, gene regulation through transcriptional insulators, and cancer. Genomic imprinting occurs in mammals before or during gamete formation. Certain genes are uniquely imprinted in each of a male and female parent; however, only one of these genes from either the maternal or paternal chromosome is expressed in their offspring; the other of which remains silent. The inheritance of imprinted genes is epigenetic, meaning these genes are regulated the same in the offspring as in the parent from which they derived, even if the nucleotide sequence encoding the gene(s) is not identical to the parental form (e.g., has accrued one or more mutations). As a result of this phenomenon, specific genes either are expressed or remain silent, based on their imprint.
While the molecular mechanism of imprinting is largely unknown, it appears that regions of chromosomes, rather than specific genes, are imprinted. Additionally, it has been determined that DNA methylation may play a role in this process. In vertebrates, methyl groups can be added to the carbon atom at position 5 in cytosine. These methyl groups are typically added when the dinucleotide CpG or groups of CpG (i.e., CpG islands) are present along a DNA sequence. CpG islands have primarily been observed in the 5′ area of expressed genes, and, in particular, the 5′ area of certain housekeeping genes (see, Bird et al., Nature 321:209-213 (1986)). It has been hypothesized that DNA methylation plays a role in gene regulation by increasing or decreasing the affinity of regulatory DNA-binding proteins, such as CTCF (see, Watson et al., Molecular Biology of the Gene, Volume II: 3rd Ed., The Benjamin/Cummings Publishing Company, Inc., Menlo, Calif. (1987)).
The process of imprinting and DNA methylation can be understood by analyzing a commonly studied imprinted gene cluster that is regulated by CTCF, which includes the closely linked imprinted genes H19 and Igf2. These genes are oppositely imprinted on each parental chromosome. Indeed, H19 is active on the maternal chromosome with Igf2 remaining silent, while on the paternal chromosome, Igf2 is active and H19 is silent. The two genes share an enhancer region located downstream of H19. Some studies have shown that the imprinting control region (ICR) of H19 is a boundary element controlled by DNA methylation. For example, it is thought that the CTCF protein binds to the unmethylated maternal ICR, which prevents the promoters located in the Igf2 gene from interacting with the enhancers downstream of the H19 gene. This results in transcriptional silencing of Igf2. If the paternal ICR is present and methylated, CTCF is prevented from binding. This allows the enhancers to contact the promoters of the paternal Igf2, allowing the gene to be transcribed.
Recent studies have indicated that abnormal imprinting could result in the activation of certain growth factors or the inactivation of tumor suppressor genes, both of which could result in the formation of cancer. Indeed, various epigenetic alterations have been associated with cancers, including global hypomethylation, hypomethylation of individual genes, and hypermethylation of CpG islands (see, Feinberg, PNAS, 98(2):392-394 (2001)). Thus, it would be beneficial to identify genes which, when abnormally imprinted, lead to the development of cancer.
Accordingly, a need remains for the identification of genes and gene products which can be shown to have a strong association with cancer. Such genes and gene products can lead to the development of novel therapeutic applications, as well as to early, sensitive and accurate methods for detecting a cancer or a predisposition to a cancer in a mammal. Moreover, such methods would enable clinicians to monitor the response of a mammal to a particular treatment with greater sensitivity and accuracy. The present invention provides such therapeutic applications and methods. These and other objects and advantages of the invention, as well as additional inventive features, will be apparent from the description of the invention provided herein.